Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model

Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK₂) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified.     

Application of Rice-Straw Biochar and Microorganisms in Nonylphenol Remediation: Adsorption-Biodegradation Coupling Relationship and Mechanism

Biochar adsorption presents a potential remediation method for the control of hydrophobic organic compounds (HOCs) pollution in the environment. It has been found that HOCs bound on biochar become less bioavailable, so speculations have been proposed that HOCs will persist for longer half-life periods in biochar-amended soil/sediment. To investigate how biochar application affects coupled adsorption-biodegradation, nonylphenol was selected as the target contaminant, and biochar derived from rice straw was applied as the adsorbent. The results showed that there was an optimal dosage of biochar in the presence of both adsorption and biodegradation for a given nonylphenol concentration, thus allowing the transformation of nonylphenol to be optimized. Approximately 47.6% of the nonylphenol was biodegraded in two days when 0.005 g biochar was added to 50 mg/L of nonylphenol, which was 125% higher than the relative quantity biodegraded without biochar, though the resistant desorption component of nonylphenol reached 87.1%. All adsorptive forms of nonylphenol (f _rap, f _slow, f _r) decreased gradually during the biodegradation experiment, and the resistant desorption fraction of nonylphenol (f _r) on biochar could also be biodegraded. It was concluded that an appropriate amount of biochar could stimulate biodegradation, not only illustrating that the dosage of biochar had an enormous influence on the half-life periods of HOCs but also alleviating concerns that enhanced HOCs binding by biochar may cause secondary pollution in biochar-modified environment.     

Purification and characterization of recombinant human testis angiotensin-converting enzyme expressed in Chinese hamster ovary cells.

Enzymatically active human testis angiotensin-converting enzyme (ACE) was expressed in Chinese hamster ovary (CHO) cells stably transfected with each of three vectors: p omega-ACE contains a full-length testis ACE cDNA under the control of a retroviral promoter; and pLEN-ACEVII and pLEN-ACE6/5, in which full-length and membrane anchor-minus testis ACE cDNAs, respectively, are under the control of the human metallothionein IIA promoter and SV40 enhancer. In every case, active recombinant human testis ACE (hTACE) was secreted in a soluble form into the culture media, up to 2.4 mg/liter in the media of metal-induced, high-producing clones transfected with one of the pLEN vectors. In addition, membrane-bound recombinant enzyme was recovered from detergent extracts of cell pellets of CHO cells transfected with either p omega-ACE or pLEN-ACE-VII. Recombinant converting enzyme was purified to homogeneity by single-step affinity chromatography of conditioned media and detergent-extracted cell pellets in 85 and 70% overall yield, respectively. Purified hTACE from all sources comigrated with the native testis isozyme on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with M(r) approximately 100 kDa. The native and recombinant proteins cross-reacted equally with anti-human kidney ACE antiserum on Western blotting. The catalytic activity of recombinant angiotensin-converting enzyme, in terms of angiotensin I and 2-furanacryloyl-Phe-Gly-Gly hydrolysis, chloride activation, and lisinopril inhibition, was essentially identical to that of the native enzyme. The facile recovery in high yield of fully active hTACE from the media of stably transfected CHO cells provides a suitable system for investigating structure-function relationships in this enzyme.